She said office interaction was vital to advance in companies, but many women were still tied to home working.
Ms Mann said it was a particular issue for mothers facing school disruptions and difficulty accessing childcare.
Earlier this year, Rishi Sunak warned about young people’s careers.
The chancellor said he doubted his banking career would have been successful if he had started it in virtual meetings, and that being in the office helped build skills.
Ms Mann, a member of the BoE’s Monetary Policy Committee that sets interest rates, said online communication was unable to replicate the spontaneous office conversations that were important for recognition and advancement in many workplaces.
She told an event hosted by Financial News magazine: “Virtual platforms are way better than they were even five years ago. But the extemporaneous, spontaneity – those are hard to replicate in a virtual setting.”
Difficulty accessing childcare and pandemic-related disruption to schooling meant many women were continuing to work from home, while it had been easier for men to return to the office.
“There is the potential for two tracks,” she said. “There’s the people who are on the virtual track and people who are on a physical track. And I do worry that we will see those two tracks develop, and we will pretty much know who’s going to be on which track, unfortunately,” she said.
Ms Mann was an economics professor and chief economist at investment bank Citi and the Organisation for Economic Co-operation and Development, before joining the BoE in September.
Businesswoman Justine Roberts, co-founder of the Mumsnet website, agreed that there was a risk women’s careers could suffer from not being in the office. But it was up to companies to be aware of this.
But the flipside, she told the BBC, was that the flexibility of home working was a huge benefit to women, and mothers in particular. Presenteeism and long-hours culture had been eroded by new ways of working.
“Let’s not forget that one of the best things to come out of [the pandemic crisis] is the ability to work flexibly,” especially for mothers juggling childcare and school runs, she said.
According to a BBC survey, just over half (56%) of women said they thought working from home would help them progress at work, as childcare and caring duties become less of a hindrance to working full-time.
In all, 65% of managers felt that working from home helps advance women’s careers. However, a quarter of the women polled said homeworking was unlikely to advance their careers.
Danielle Harmer, chief people officer at insurance giant Aviva, said companies need to set out a framework to ensure that people working remotely are not an afterthought for company bosses. Otherwise, she said, career prospects and the gender pay gap would suffer.
“I think if organisations leave it up to their employees, you could have a potential situation where those with caring responsibilities, who tend to be female, tend to work from home more often, and we look back in two years and think: hang on a second, why has the gender pay gap widened? Or why are female promotions slowing down a little?” she said.
“It’s taken us a long time to make progress on things like the gender pay gap, and I think it would be terrible if we went backwards on it.”
The Office for National Statistics (ONS) said British businesses reported that on average 60% of their staff were fully back at their normal place of work. About one-in-six employees are estimated to be using a hybrid model of working, the ONS said.
“The buzz around the office and the buzz around the city is fantastic.”
“I don’t think we should be micromanaging companies but there is a very strong message the the city is open,” he added.
However, proportions vary widely by sector. In professional services, 34% of staff are in the office, 24% are fully working from home, and 35% are doing a mix, the ONS said.
Separate ONS data showed a slightly higher percentage of male workers than females worked from home for at least some of the time in late October.
Previous ONS analysis showed women were more likely than men to say working from home allowed them more time to work, with fewer distractions. But men said working from home helped them come up with new ideas, while women found it a hindrance.